Introduction to Bioinformatics

This course covers computational techniques for mining the large amount of information produced by recent advances in biology, such as genome sequencing and microarrray technologies. Main topics of the course include: DNA and protein sequence alignment, sequence motifs/patterns, phylogenetic trees, protein structures: prediction, alignment, classification microarray data analysis: normalization, clustering and biological networks.


Automated biological data acquisition and integration using machine learning techniques
Çarkacıoğlu, Levent; Atalay, Mehmet Volkan; Department of Computer Engineering (2009)
Since the initial genome sequencing projects along with the recent advances on technology, molecular biology and large scale transcriptome analysis result in data accumulation at a large scale. These data have been provided in different platforms and come from different laboratories therefore, there is a need for compilation and comprehensive analysis. In this thesis, we addressed the automatization of biological data acquisition and integration from these non-uniform data using machine learning techniques....
A survey on piecewise-linear models of regulatory dynamical systems
Öktem, Hüseyin Avni (Elsevier BV, 2005-11-01)
Recent developments in understanding the various regulatory systems, especially the developments in biology and genomics, stimulated an interest in modelling such systems. Hybrid systems, originally developed for process control applications, provide advances in modelling such systems. A particular class of hybrid systems which are relatively simpler to analyze mathematically but still capable of demonstrating the essential features of many non-linear dynamical systems is piecewise-linear systems. Implement...
A deep learning approach for the transonic flow field predictions around airfoils
Duru, Cihat; Alemdar, Hande; Baran, Özgür Uğraş (2022-01-01)
Learning from data offers new opportunities for developing computational methods in research fields, such as fluid dynamics, which constantly accumulate a large amount of data. This study presents a deep learning approach for the transonic flow field predictions around airfoils. The physics of transonic flow is integrated into the neural network model by utilizing Reynolds-averaged Navier–Stokes (RANS) simulations. A detailed investigation on the performance of the model is made both qualitatively and quant...
A survey on persistence landscape theory
Gürses, Selçuk; Pamuk, Semra; Department of Mathematics (2022-7)
Topological data analysis (TDA) consists of a growing collection of techniques that reveal the shape of data. These techniques may be especially useful for comprehend ing global features of high-dimensional data that are inaccessible via other methods. The usage of TDA has been constrained by the difficulties of merging the subject’s primary tool, the barcode or persistence diagram, with statistics and machine learning. The persistence landscape is a stable topological summary that is easily combinable with...
Computational representation of protein sequences for homology detection and classification
Oğul, Hasan; Mumcuoğlu, Ünal Erkan; Department of Information Systems (2006)
Machine learning techniques have been widely used for classification problems in computational biology. They require that the input must be a collection of fixedlength feature vectors. Since proteins are of varying lengths, there is a need for a means of representing protein sequences by a fixed-number of features. This thesis introduces three novel methods for this purpose: n-peptide compositions with reduced alphabets, pairwise similarity scores by maximal unique matches, and pairwise similarity scores by...
Citation Formats
T. Can, “Introduction to Bioinformatics,” 00, 2009, Accessed: 00, 2020. [Online]. Available: